AMBER LIBRARIES

I have been foiled in my attempt to build a phosphoserine library for AMBER despite the fact that I know that others seems to have done it. Could anyone comment one my strategy to build this library? I am sure I am close, but ... you know how working with code that you are just learning goes.... anyway I would also like to know the relationships between the many library files as well, as my misunderstanding might be at the root cause of my errors.

Here is what I did.

1) Build the residue in Insight, used its optimization to relax the molecule to get appropriate bond angles, and lengths
2) Run antechamber to get a sep.prepin library fragment to use in tleap
3) Goal: Run tleap to generate a general prmtop file for the AMBER molecular simulation
4) Goal: Run sander

----------------------------------
Result of 2:
0 0 2

This is a remark line
molecule.res
SEP XYZ 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 O2P o S 3 2 1 1.540 111.208 180.000 0.000
5 P p5 S 4 3 2 1.592 70.512 -161.384 0.000
6 O1P oh S 5 4 3 1.535 109.613 -116.390 0.000
7 H1P ho E 6 5 4 0.958 104.360 -50.138 0.000
8 O3P oh S 5 4 3 1.536 110.667 124.265 0.000
9 H3P ho E 8 5 4 0.955 104.575 174.086 0.000
10 OG os S 5 4 3 1.615 109.785 3.781 0.000
11 CB c3 S 10 5 4 1.450 122.662 56.061 0.000
12 HB2 h1 E 11 10 5 1.111 110.009 65.687 0.000
13 HB3 h1 E 11 10 5 1.111 109.974 -48.967 0.000
14 CA c3 M 11 10 5 1.546 111.429 -171.456 0.000
15 N n2 M 14 11 10 1.494 108.382 55.875 0.000
16 HN h E 15 14 11 1.031 108.234 -55.713 0.000
17 HA h1 E 14 11 10 1.109 107.616 173.545 0.000
18 C c M 14 11 10 1.558 111.435 -71.121 0.000
19 O o E 18 14 11 1.224 122.962 -99.193 0.000


LOOP

IMPROPER

DONE
STOP

This seems to be ok, I had solved a number of geometry problems and nomenclature problems last week and the data seems resonable. However, I had to hand edit this file because the original antechamber output kept calling PO(4-) atoms M for main backbone and not S for sidechain (maybe a sign that I have done this wrong too)
----------------------------------------------
Result of 3:
Loading Prep file: ./sep.prepin
Loading parameters: ./frcmod
Reading force field mod type file (frcmod)
Loading PDB file: ./leap_temp_pro.apdb
Added missing heavy atom: .R.A
total atoms in file: 290
Leap added 3 missing atoms according to residue templates:
1 Heavy
2 H / lone pairs
Checking Unit.
WARNING: The unperturbed charge of the unit: 2.000000 is not zero.

-- ignoring the warning.

Building topology.
Building atom parameters.
For atom: .R.A Could not find type: o
For atom: .R.A

Could not find type: p5
For atom: .R.A Could not find type: oh
For atom: .R.A Could not find type: ho
For atom: .R.A Could not find type: oh
For atom: .R.A Could not find type: ho
For atom: .R.A Could not find type: os
For atom: .R.A Could not find type: c3
For atom: .R.A Could not find type: h1
For atom: .R.A Could not find type: h1
For atom: .R.A Could not find type: c3
For atom: .R.A Could not find type: n2
For atom: .R.A Could not find type: h
For atom: .R.A Could not find type: h1
For atom: .R.A Could not find type: c
For atom: .R.A Could not find type: o
Parameter file was not saved.

But the problem seems to be with the names O, P5, OH, etc and that is what antechamber produced! I then looked through files like

all_amino94.lib all_amino02.lib
parm94.dat
all_amino94.in

I tried capitalization, renaming, etc and been lead astray by things like the fact the _every_ standard residue had a nitrogen - hydrogen label H and leap _wouldnot_ take that for my new residue ... it wanted to be labeled HN. Why, I am not sure but presumably there is a list of aliases from H -> HN for predefined residues.

-----------------------
Then I tried to modify the core library directly, that is all_amino94.lib That is almost complete, but apparently the section :

!entry.SER.unit.positions table dbl x dbl y dbl z
3.325770 1.547909 -1.607257E-06
3.909407 0.723611 -2.739904E-06
3.970048 2.845795 -1.312144E-07
3.671663 3.400129 -0.889820
3.576965 3.653838 1.232143
2.496995 3.801075 1.241379
3.877484 3.115795 2.131197
4.230753 4.925145 1.196917
3.983305 5.433814 1.972562
5.485541 2.705207 -4.398851E-06
6.008824 1.593175 -8.449829E-06

as a tempate for my new !entry SEP ...

needs to have the HN-N-CA-C in a plane and so am I making that transformation. When I place a general set of coordinated in leap said that the file was not a valid library.

----------------------

Am I following the process correctly? As a minor note I have been able to build libraries for both Dyana and MolMol and they are working. Any comments would be greatly appreciated.

# posted by xcrabturtle : 6:37 AM

Using the HSG Convention in tLeap / Amber

I have updated the leaprc.ff99 file so that the nomenclature of HSG and HG is mapped for the amino acid residue cysteine. This was done using the addPdbAtomMap command as shown below.

I am using .../dat/leap/lib/all_aminont02.lib and it has these lines:

!entry.NCYS.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"N" "N3" 0 1 131072 1 7 0.190200
"H1" "H" 0 1 131072 2 1 0.205600
"H2" "H" 0 1 131072 3 1 0.205600
"H3" "H" 0 1 131072 4 1 0.205600
"CA" "CT" 0 1 131072 5 6 0.021300
"HA" "HP" 0 1 131072 6 1 0.057800
"CB" "CT" 0 1 131072 7 6 -0.031600
"HB2" "H1" 0 1 131072 8 1 0.065500
"HB3" "H1" 0 1 131072 9 1 0.065500
"SG" "SH" 0 1 131072 10 16 -0.246400
"HSG" "HS" 0 1 131072 11 1 0.159100 <--- Clue
"C" "C" 0 1 131072 12 6 0.683700
"O" "O" 0 1 131072 13 8 -0.581900

This is where I got the clue to use HSG and not HG

Following the advise of Bill Ross I added
addPdbAtomMap {
# Cysteine HSG convention
{ "HG" "HSG" }
}
and diff'ed the amber.pdb and prmtop file and got a
perfect match between the input PDB file using
HSG (the one I originally got to work) and
the HG (with addPdbAtomMap fix ).

Fortunetly the serine remained HG
so apparently the leap figured out that the HG to
HSG change only applied to the CYS

Thanks very much JWCraft

PS actually all the libs had the HSG convention

11% pwd
.. AMBER/IRIX64/amber7/dat/leap/lib
12% grep HSG *
all_aminoct02.lib: "HSG" "HS" 0 1 131072 9 1 0.157700
all_aminoct02.lib: "HSG" "HS" 0 -1 0.0
all_aminoct02EP.lib: "HSG" "HS" 0 1 131072 11 1 0.161700
all_aminoct02EP.lib: "HSG" "HS" 0 -1 0.0
all_aminoct91.lib: "HSG" "HS" 0 1 131072 9 1 0.135000
all_aminoct91.lib: "HSG" "HS" 0 -1 0.0
all_aminoct94.lib: "HSG" "HS" 0 1 131072 9 1 0.206800
all_aminoct94.lib: "HSG" "HS" 0 -1 0.0
all_aminont02.lib: "HSG" "HS" 0 1 131072 11 1 0.159100
all_aminont02.lib: "HSG" "HS" 0 -1 0.0
all_aminont02EP.lib: "HSG" "HS" 0 1 131072 13 1 0.164200
all_aminont02EP.lib: "HSG" "HS" 0 -1 0.0
all_aminont91.lib: "HSG" "HS" 0 1 131072 11 1 0.135000
all_aminont91.lib: "HSG" "HS" 0 -1 0.0
all_aminont94.lib: "HSG" "HS" 0 1 131072 11 1 0.197500
all_aminont94.lib: "HSG" "HS" 0 -1 0.0
pro-dna91.nmr.off: "HSG" "HS" 0 1 131072 9 1 0.135000
pro-dna91.nmr.off: "HSG" "HS" 0 -1 0.0
pro-dna91.nmr.off: "HSG" "HS" 0 1 131072 11 1 0.135000
pro-dna91.nmr.off: "HSG" "HS" 0 -1 0.0